Organism : Campylobacter jejuni | Module List :
Cj0901

putative amino acid ABC tansporter permease protein (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
ABC-type amino acid transport system, permease component cog/ cog
dicarboxylic acid transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
sodium:dicarboxylate symporter activity go/ molecular_function
HEQRo_perm_3TM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj0901
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Cj0901!

Warning: Cj0901 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7566 4.10e+02 GGCGAATTTTGTGGTAGAATTAC
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7567 3.70e+03 CAGCTTAATGAGC
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7636 1.90e+03 A.cttt.tcCaAaAtcTtAcc
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7637 3.90e+04 aGTGGG
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for Cj0901

Cj0901 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type amino acid transport system, permease component cog/ cog
dicarboxylic acid transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
sodium:dicarboxylate symporter activity go/ molecular_function
HEQRo_perm_3TM tigr/ tigrfam
Module neighborhood information for Cj0901

Cj0901 has total of 41 gene neighbors in modules 92, 127
Gene neighbors (41)
Gene Common Name Description Module membership
Cj0069 Cj0069 hypothetical protein Cj0069 (NCBI ptt file) 69, 127
Cj0103 atpF ATP synthase F0 sector B subunit (NCBI ptt file) 125, 127
Cj0114 Cj0114 putative periplasmic protein (NCBI ptt file) 91, 127
Cj0144 Cj0144 methyl-accepting chemotaxis signal transduction protein (NCBI ptt file) 8, 127
Cj0401 lysS lysyl-tRNA synthetase (NCBI ptt file) 42, 127
Cj0403 Cj0403 hypothetical protein Cj0403 (NCBI ptt file) 127, 170
Cj0420 Cj0420 putative periplasmic protein (NCBI ptt file) 102, 127
Cj0594c Cj0594c putative periplasmic protein (NCBI ptt file) 89, 92
Cj0600 Cj0600 hypothetical protein Cj0600 (NCBI ptt file) 92, 162
Cj0604 Cj0604 hypothetical protein Cj0604 (NCBI ptt file) 119, 127
Cj0726c corA magnesium and cobalt transport protein (NCBI ptt file) 86, 127
Cj0806 dapA dihydrodipicolinate synthase (NCBI ptt file) 127, 137
Cj0901 Cj0901 putative amino acid ABC tansporter permease protein (NCBI ptt file) 92, 127
Cj1119c wlaM putative integral membrane protein (NCBI ptt file) 41, 127
Cj1120c wlaL putative sugar epimerase/dehydratase (NCBI ptt file) 127, 157
Cj1121c wlaK putative aminotransferase (degT family) (NCBI ptt file) 118, 127
Cj1141 neuB1 N-acetylneuraminic acid synthetase (NCBI ptt file) 24, 92
Cj1154c Cj1154c small hydrophobic protein (NCBI ptt file) 47, 127
Cj1208 Cj1208 hypothetical protein Cj1208 (NCBI ptt file) 92, 128
Cj1317 neuB3 N-acetylneuraminic acid synthetase (NCBI ptt file) 65, 127
Cj1340c Cj1340c hypothetical protein Cj1340c (1318 family) (NCBI ptt file) 92, 124
Cj1341c Cj1341c hypothetical protein Cj1341c (1318 family) (NCBI ptt file) 92, 117
Cj1342c Cj1342c hypothetical protein Cj1342c (617 family) (NCBI ptt file) 92, 124
Cj1343c Cj1343c putative periplasmic protein (NCBI ptt file) 92, 106
Cj1344c Cj1344c putative glycoprotease (NCBI ptt file) 92, 149
Cj1345c Cj1345c putative periplasmic protein (NCBI ptt file) 11, 92
Cj1346c dxr putative 1-deoxy-D-xylulose 5-phosphate reductoisomerase (NCBI ptt file) 47, 92
Cj1347c cdsA phosphatidate cytidylyltransferase (NCBI ptt file) 11, 92
Cj1348c Cj1348c putative coiled-coil protein (NCBI ptt file) 75, 92
Cj1349c Cj1349c possible fibronectin/fibrinogen-binding protein (NCBI ptt file) 47, 92
Cj1350 mobA putative molybdopterin-guanine dinucleotide biosynthesis protein (NCBI ptt file) 92, 124
Cj1420c Cj1420c hypothetical protein Cj1420c (NCBI ptt file) 120, 127
Cj1421c Cj1421c possible sugar transferase (NCBI ptt file) 92, 99
Cj1484c Cj1484c putative membrane protein (NCBI ptt file) 79, 92
Cj1502c putP sodium/proline symporter (NCBI ptt file) 91, 127
Cj1516 Cj1516 putative periplasmic oxidoreductase (NCBI ptt file) 127, 161
Cj1563c Cj1563c putative transcriptional regulator (NCBI ptt file) 59, 92
Cj1603 hisF cyclase (NCBI ptt file) 13, 127
Cj1640 Cj1640 hypothetical protein Cj1640 (NCBI ptt file) 92, 102
Cj1646 iamB putative ABC transport system permease protein (NCBI ptt file) 7, 92
Cj1668c Cj1668c putative periplasmic protein (NCBI ptt file) 92, 132
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for Cj0901
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend